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solvent accessibility & WRITE_DATA



Dear Modeller users & developers,

I would like to use the capability of modeller to calculate different kind of solvent accessibility data with the WRITE_DATA command. I can get the *.psa file and the *.sol file using the script shown below (practically identical with the example in the manual).
Now my questions:

o what are the units of the numbers given in the *.psa file?
I suppose that the "Sum" coloumns give the accessible surface in square Angstrom. The "Per." coloumns are supposed to the accessible surface area in percent of the total surface? Why do I get values above 100 in many cases then?

o How should the ACCESSIBILITY_TYPE parameter of WRITE_DATA be used to write different kind of accessibility dat to the Biso coloumn of the *.sol file? As far as I understand the manual the ACCESSIBILITY_TYPE parameter can be used to influence this part of the *.sol output file? I tried various things without any effect.

o What are the numbers written to the *.sol file with the script below?

Thanks a lot in advance,
Oliver
____________________________________________________________

Oliver Hucke (PostDoc)
Biomolecular Structure Center
Dept. of Biochemistry
University of Washington
Health Sciences Building K-418C
1959 NE Pacific Ave Seattle, WA 98195
T:(206)685-7046
_______________________________


My input script:
------------------------------------------------------------
SET OUTPUT_CONTROL = 1 1 1 1 0

READ_TOPOLOGY FILE = '$(LIB)/top_heav.lib'
SET HETATM_IO = off, WATER_IO = off

READ_MODEL FILE = 'protein'

SET RADII_FACTOR = 1.0

WRITE_DATA FILE = 'protein', OUTPUT = 'PSA'
--------------------------------------------------------------

Start of the protein.psa file:
--------------------------------------------------------------
#COLUMNS S S S N N N N N N N N N N
# produced by MODELLER
#
# File of summed (Sum) and % (per.) accessibilities
# probe radius       :   1.400
# integration step   :   0.100
# water included     : ?
# hetatom included   : ?
# accessibility type : CONTACT
# number of residues :     730
#
# Res Res All atoms Non P side Polar Side Total Side Main Chain # Num type Sum Per. Sum Per. Sum Per. Sum Per. Sum Per. ACCESS 55 PHE A 75.12 123.5 50.74 98.4 0.00 0.0 50.74 98.4 24.38 262.7 ACCESS 56 LEU A 19.62 34.7 16.14 34.6 0.00 0.0 16.14 34.6 3.47 35.0 ACCESS 57 SER A 20.64 61.1 11.84 75.1 7.67 97.5 19.51 82.6 1.13 11.1 ACCESS 58 LEU A 3.76 6.6 2.99 6.4 0.00 0.0 2.99 6.4 0.76 7.7 ACCESS 59 ASP A 31.28 79.4 9.54 59.8 13.93 103.7 23.47 79.8 7.81 78.3
--------------------------------------------------------------------------------------------------

Start of the corresponding *.sol file:
---------------------------------------------------------

# produced by MODELLER
#
# File of atomic accessibilities
# probe radius       :   1.400
# integration step   :   0.100
# water included     : ?
# hetatom included   : ?
# accessibility type : CONTACT
# number of residues :     730
ATOM      1 N    PHE A  55     107.149  -1.404  53.483     1.650  14.140
ATOM      2 CA   PHE A  55     106.564  -2.771  53.570     1.800   1.890
ATOM      3 C    PHE A  55     106.502  -3.415  52.180     1.800   1.008
ATOM      4 O    PHE A  55     107.505  -3.970  51.725     1.550   9.229
ATOM      5 CB   PHE A  55     105.182  -2.745  54.253     1.800   2.554
ATOM      6 CG   PHE A  55     105.162  -3.402  55.622     1.800   0.319
ATOM      7 CD1  PHE A  55     104.233  -4.411  55.914     1.800   7.619
ATOM      8 CD2  PHE A  55     106.077  -3.026  56.615     1.800   4.669
ATOM      9 CE1  PHE A  55     104.214  -5.040  57.174     1.800  11.557


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